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Under FreeBSD (pfSense is based on FreeBSD and has nothing to do with Linux) you can create multiple wlan interfaces based on the physical interface, then connect them to various APs. For instance, if you have an Atheros card in your computer (and it isn't renamed):

ok, but how do applications choose an interface resp. how can I force an app to use a specific interface?
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Trass3rJun 6 '12 at 12:53

Application do not choose an interface, the OS handles that. The best an App can do is select an IP associated with an interface. If you mean to ask how you can get an App to send traffic to different gateways you'd have to screw with routing tables and possibly start the app with altered network views. That's outside the scope of this Question so you'd have to ask a New Question.
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Chris SJun 6 '12 at 18:21

Is there a way to do this in Linux? Linux ifconfig do not have "create" keyword.
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V3ss0nApr 2 '13 at 14:42

Linux can connect to multiple WiFi networks, but they have to be on the same channel. I'm not familiar with the process however. There may be an existing Q/A on Server Fault, or Super User or Unix & Linux too.
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Chris SApr 2 '13 at 15:26